Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ---- echo=T, eval=F----------------------------------------------------------
# # Install FAMetA
# install.packages("FAMetA", dependencies = c("Depends", "Imports"))
#
# # load library
# library(FAMetA)
#
## ---- echo=T, eval=F----------------------------------------------------------
# library(FAMetA)
# library(tools)
#
# # Example files can be found at
# # <https://drive.google.com/drive/folders/1-mhqBd6W8VJkIYwVuIOr2Gn4Z9vBUN9-?usp=sharing>.
# # This dataset contains 12 samples of linfocites grown in culture media
# # supplemented with 13Cglc, 13Cglc+iFASN, 13Cglc+iSCD and 13Cglc+iFADS2
# # (3 replicates of each condition), 2 blank samples and 3 injections of a
# # standards mix.
#
# #==============================================================================#
# # Data pre-processing using LipidMS package
# #==============================================================================#
#
# #=================#
# # Read metadata
#
# metadata <- read.csv("samples.csv", header = T, sep=",")
#
# # check file names (they must include .mzXML)
# if (!all(file_ext(metadata$sample) == "mzXML")){
# metadata$sample[file_ext(metadata$sample) != "mzXML"] <-
# paste(metadata$sample[file_ext(metadata$sample) != "mzXML"], ".mzXML", sep="")
# }
#
#
# #=================#
# # Set processing parameters
#
# # Peak-picking
# polarity <- "negative"
# dmzagglom <- 15 # dmz and drt to generate bins/partitions for peak-picking
# drtagglom <- 200 # max rt window for bins
# drtclust <- 100 # drt window for clustering (redefines previous bins)
# minpeak <- 8 # min number of points to define a peak (MS1, MS2)
# minint <- 100000 # at least minpeak points must have minint intensity
# drtgap <- 5 # max rt gap to fill missing points in a peak
# drtminpeak <- 8 # min width of a peak when there are more than 1 peak in a EIC
# drtmaxpeak <- 30 # max rt window for a EIC
# recurs <- 10 # max number of peaks in a EIC
# sb <- 5 # signal-to-baseline ratio (MS1, MS2)
# sn <- 5 # signal-to-noise ratio
# weight <- 2 # weight to assign new peaks
# dmzIso <- 5 # dmz for isotopes search
# drtIso <- 5 # drt for isotopes search
#
# parallel <- TRUE # parallel processing
# ncores <- 4 # number of cores
#
#
# #=================#
# # Peak-picking
# msbatch <- batchdataProcessing(metadata = metadata,
# polarity = polarity,
# dmzagglom = dmzagglom,
# drtagglom = drtagglom,
# drtclust = drtclust,
# minpeak = minpeak,
# drtgap = drtgap,
# drtminpeak = drtminpeak,
# drtmaxpeak = drtmaxpeak,
# recurs = recurs,
# sb = sb,
# sn = sn,
# minint = minint,
# weight = weight,
# dmzIso = dmzIso,
# drtIso = drtIso,
# parallel = parallel,
# ncores = ncores)
## ---- echo=T, eval=F----------------------------------------------------------
# #=================#
# # Batch processing
# dmzalign <- 10 # max dmz and rt to group peaks for alignment
# drtalign <- 60 # max rt window for clustering in alignment
# span <- 0.2 # span for alignment
# minsamplesfracalign <- 0.50 # min fraction of samples represented in a peak group to be used for alignment
# dmzgroup <- 10 # max dmz and rt to group peaks for grouping
# drtagglomgroup <- 50 # max rt window for clustering in grouping
# drtgroup <- 10 # max rt difference within a peak group
# minsamplesfracgroup <- 0.20 # min fraction of samples represented in a peak group to be kept
#
#
# #=================#
# # Alignment
# msbatch <- alignmsbatch(msbatch, dmz = dmzalign, drt = drtalign, span = span,
# minsamplesfrac = minsamplesfracalign,
# parallel = parallel, ncores = ncores)
#
# #=================#
# # Grouping
# msbatch <- groupmsbatch(msbatch, dmz = dmzgroup, drtagglom = drtagglomgroup,
# drt = drtgroup, minsamplesfrac = minsamplesfracgroup,
# parallel = parallel, ncores = ncores)
#
#
# #=================#
# # Save msbatch
# save(msbatch, "msbatch.rda.gz", compress = TRUE)
#
#
# # If any other external software is used for processing, data can be loaded from
# # a csv file using the following function:
# # fadata <- readfadatafile("externafadata.csv", sep=",", dec=".")
#
# # In this case, go directly to data correction step.
## ---- echo=T, eval=F----------------------------------------------------------
# #==============================================================================#
# # FA annotation
# #==============================================================================#
#
# #=================#
# # Annotate FA
# msbatch <- annotateFA(msbatch, dmz = 5)
#
# #=================#
# # plot peaks from identified FAs to check them
# plots <- plotFA(msbatch, dmz = 10)
#
# pdf("FAs.pdf")
# for (p in 1:length(plots)){
# print(plots[[p]])
# }
# dev.off()
#
# #=================#
# # export annotations for curation
# write.csv(msbatch$fas, file="faid.csv", row.names=FALSE)
#
## ---- echo=T, eval=F----------------------------------------------------------
# #==============================================================================#
# # FA curation
# #==============================================================================#
#
# #=================#
# # read csv file with modified annotations
# faid <- read.csv("faid_curated.csv", sep=",", dec=".")
#
# #=================#
# # change FA annotations
# msbatch <- curateFAannotations(msbatch, faid)
#
# #=================#
# # plot FA peaks again to check identities
# plots <- plotFA(msbatch, dmz = 10)
#
# pdf("FAs_curated.pdf")
# for (p in 1:length(plots)){
# print(plots[[p]])
# }
# dev.off()
## ---- echo=T, eval=F----------------------------------------------------------
# #==============================================================================#
# # Search FA isotopes and get the fadata object
# #==============================================================================#
# fadata <- searchFAisotopes(msbatch, dmz = 10, coelCutoff = 0.6)
#
#
# # if you want to save fadata in a csv to subset it for example:
# df <- cbind(rbind(fadata$fattyacids, data.frame(Compound="IS", Label="")),
# rbind(fadata$intensities, fadata$IS))
# df <- rbind(c("", "sampletype", fadata$metadata$sampletype),
# c("Compound", "Label", colnames(fadata$intensities)), df)
# write.table(df, file="fadata.csv", sep=",", col.names = FALSE, row.names = FALSE)
#
# # and then, you could read it again using:
# fadata <- readfadatafile("fadata.csv", sep=",", dec=".")
## ---- echo=T, eval=F----------------------------------------------------------
# #==============================================================================#
# # Import FA data
# #==============================================================================#
# inputfile <- "externalfadata.csv"
# fadata <- readfadatafile(inputfile, sep=",", dec=".")
## ---- echo=T, eval=F----------------------------------------------------------
# #==============================================================================#
# # Data correction
# #==============================================================================#
# fadata <- dataCorrection(fadata, blankgroup = "Blank")
#
# # Alternatively, to add external normalization:
# # fadata <- dataCorrection(fadata, blankgroup = "blank",
# # externalnormalization = "protein")
## ---- echo=T, eval=F----------------------------------------------------------
# #==============================================================================#
# # Metabolic analysis
# #==============================================================================#
#
# #=================#
# # Synthesis analysis
# fadata <- synthesisAnalysis(fadata=fadata, R2Thr = 0.95, maxiter = 1e3,
# maxconvergence = 100, startpoints = 5)
#
# # If inhibitors have been used, make sure D2 has not been underestimated. If so,
# # D2 could be set as the one calculated for 13-Glc Control samples to improve
# # the results:
#
# # D2 <- fadata$synthesis$results$D2[fadata$synthesis$results$FA == "FA(16:0)"]
# # fadata$synthesis$results$Group[fadata$synthesis$results$FA == "FA(16:0)"]
#
# # D2[4:12] <- rep(mean(D2[1:3]))
#
# # relaunch synthesis analysis fixing D2
# # fadata <- synthesisAnalysis(fadata=fadata, R2Thr = 0.95, maxiter = 1e3,
# # maxconvergence = 100, startpoints = 5, D2 = D2)
#
#
# # Explore results
# View(fadata$synthesis$results)
# View(fadata$synthesis$predictedValues)
# pdf("plotsSynthesis.pdf")
# for (f in 1:length(fadata$synthesis$plots)){
# for (s in 1:length(fadata$synthesis$plots[[f]])){
# print(fadata$synthesis$plots[[f]][[s]])
# }
# }
# dev.off()
#
# # to use multinomial distribution without over dispersion, set P parameter to 0
# fadata <- synthesisAnalysis(fadata=fadata, R2Thr = 0.95, maxiter = 1e3,
# maxconvergence = 100, startpoints = 5, P = 0)
#
## ---- echo=T, eval=F----------------------------------------------------------
# #=================#
# # Elongation analysis
# fadata <- elongationAnalysis(fadata, R2Thr = 0.95, maxiter = 1e4,
# maxconvergence=100, startpoints = 5, DThr = 0.1)
#
#
# # Explore results
# View(fadata$elongation$results)
# View(fadata$elongation$predictedValues)
# pdf("plotsElongation.pdf")
# for (f in 1:length(fadata$elongation$plots)){
# for (s in 1:length(fadata$elongation$plots[[f]])){
# print(fadata$elongation$plots[[f]][[s]])
# }
# }
# dev.off()
## ---- echo=T, eval=F----------------------------------------------------------
# #=================#
# # Desaturation analysis
# fadata <- desaturationAnalysis(fadata)
#
# # Explore results
# View(fadata$desaturations$results)
## ---- echo=T, eval=F----------------------------------------------------------
# #=================#
# # Summarize results
# fadata <- summarizeResults(fadata, controlgroup = "Control13Cglc")
#
# #=================#
# # Save fadata
# save(fadata, file="fadata.rda")
#
#
#
# #=================#
# # Export results
# write.csv(fadata$results$results, file = "results.csv", row.names=FALSE)
# write.csv(fadata$results$summary, file = "summary.csv")
# write.table(rbind(fadata$metadata$sampletype,
# colnames(fadata$mid),
# fadata$mid),
# file = "mid.csv", sep=",", col.names = FALSE)
# write.table(rbind(fadata$metadata$sampletype,
# colnames(fadata$synthesis$predictedValues),
# fadata$synthesis$predictedValues),
# file = "predictedmid.csv", sep=",", col.names = FALSE)
#
#
# pdf("relativepoolsizeRaw.pdf")
# print(fadata$results$heatmaps$relativepoolsize$raw$plot)
# dev.off()
#
# write.table(rbind(fadata$metadata$sampletype,
# colnames(fadata$results$heatmaps$relativepoolsize$raw$values),
# fadata$results$heatmaps$relativepoolsize$raw$values),
# file = "relativepoolsizeRaw.csv", sep=",", col.names = FALSE)
#
#
# pdf("relativepoolsizeZscore.pdf")
# print(fadata$results$heatmaps$relativepoolsize$zscore$plot)
# dev.off()
#
# write.table(rbind(fadata$metadata$sampletype,
# colnames(fadata$results$heatmaps$relativepoolsize$raw$values),
# fadata$results$heatmaps$relativepoolsize$zscore$values),
# file = "relativepoolsizeZscore.csv", sep=",", col.names = FALSE)
#
# if ("log2FC" %in% names(fadata$results$heatmaps$relativepoolsize)){
# pdf("relativepoolsizeLog2FC.pdf")
# print(fadata$results$heatmaps$relativepoolsize$log2FC$plot)
# dev.off()
#
# write.table(rbind(fadata$metadata$sampletype,
# colnames(fadata$results$heatmaps$relativepoolsize$log2FC$values),
# fadata$results$heatmaps$relativepoolsize$log2FC$values),
# file = "relativepoolsizeLog2FC.csv", sep=",", col.names = FALSE)
# }
#
# pdf("resultsRaw_endogenouslySynthesized.pdf")
# print(fadata$results$heatmaps$synthesized$raw$plot)
# dev.off()
#
# write.table(rbind(fadata$metadata$sampletype,
# colnames(fadata$results$heatmaps$synthesized$raw$values),
# fadata$results$heatmaps$synthesized$raw$values),
# file = "resultsRaw_endogenouslySynthesized.csv", sep=",",
# col.names = FALSE)
#
#
# if ("log2FC" %in% names(fadata$results$heatmaps$synthesized)){
# pdf("resultsLog2FC_endogenouslySynthesized.pdf")
# print(fadata$results$heatmaps$synthesized$log2FC$plot)
# dev.off()
#
# write.table(rbind(fadata$metadata$sampletype,
# colnames(fadata$results$heatmaps$synthesized$log2FC$values),
# fadata$results$heatmaps$synthesized$log2FC$values),
# file = "resultsLog2FC_endogenouslySynthesized.csv", sep=",",
# col.names = FALSE)
# }
#
#
# #=================#
# # Isotopologue distributions: observed vs predicted
#
# pdf("isotopologueDistributions.pdf")
# for (f in 1:length(fadata$synthesis$plots)){
# for (s in 1:length(fadata$synthesis$plots[[f]])){
# print(fadata$synthesis$plots[[f]][[s]])
# }
# }
# for (f in 1:length(fadata$elongation$plots)){
# for (s in 1:length(fadata$elongation$plots[[f]])){
# print(fadata$elongation$plots[[f]][[s]])
# }
# }
# dev.off()
#
#
#
# #=================#
# # Reorganized tables for synthesis and elongation parameters (S16, E1, E2, E3,
# # E4 and E5)
#
# write.table(rbind(fadata$metadata$sampletype,
# colnames(fadata$results$allparameters$S16),
# fadata$results$allparameters$S16),
# file = "S16.csv", sep=",", col.names = FALSE)
#
# write.table(rbind(fadata$metadata$sampletype,
# colnames(fadata$results$allparameters$E1),
# fadata$results$allparameters$E1),
# file = "E1.csv", sep=",", col.names = FALSE)
#
# write.table(rbind(fadata$metadata$sampletype,
# colnames(fadata$results$allparameters$E2),
# fadata$results$allparameters$E2),
# file = "E2.csv", sep=",", col.names = FALSE)
#
# write.table(rbind(fadata$metadata$sampletype,
# colnames(fadata$results$allparameters$E3),
# fadata$results$allparameters$E3),
# file = "E3.csv", sep=",", col.names = FALSE)
#
# write.table(rbind(fadata$metadata$sampletype,
# colnames(fadata$results$allparameters$E4),
# fadata$results$allparameters$E4),
# file = "E4.csv", sep=",", col.names = FALSE)
#
# write.table(rbind(fadata$metadata$sampletype,
# colnames(fadata$results$allparameters$E5),
# fadata$results$allparameters$E5),
# file = "E5.csv", sep=",", col.names = FALSE)
## ---- echo=T, eval=F----------------------------------------------------------
# #=================#
# # Customize parameters database
# parameters <- FAMetA::parameters
#
# # Add a new unknown FA(18:1)
# newrow <- data.frame(FattyAcid = "FA(18:1)nv",
# M = 18,
# S16 = 1,
# E1 = 1,
# E2 = 0,
# E3 = 0,
# E4 = 0,
# E5 = 0)
#
#
# parameters <- data.frame(rbind(parameters, newrow))
# parameters <- parameters[order(parameters$FattyAcid),]
# View(parameters)
#
# # Change fatty acid settings: add E1 step for FA(18:3)n6
# parameters$E1[parameters$FattyAcid == "FA(18:3)n6"] <- 1
#
#
# # Then add the parameters argument to elongationAnalysis and summarizeResults
# # functions
# fadata <- elongationAnalysis(fadata, R2Thr = 0.95, maxiter = 1e4,
# maxconvergence=100, startpoints = 5, D2Thr = 0.1,
# parameters = parameters)
#
# fadata <- FAMetA:::summarizeResults(fadata, controlgroup = "H460_13Cglc",
# parameters = parameters)
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